Spectroscopic study and molecular simulation: Bovine serum albumin binding with anticancer Pt complex of amyl dithiocarbamate ligand

Until now, many methods have been proposed to treat cancer, such as radiation therapy and drug therapy, but none of them have caused a complete cure for cancer. Heavy metal complexes such as cisplatin are among the compounds used as drugs in chemotherapy against cancer cells. These compounds cause cell death and have anti-cancer properties, but they have side effects. The biochemical mechanism of cisplatin is related to its interaction with DNA through covalent binding. To reduce the toxicity of metallodrugs, new complexes can be designed containing S, S- bidentate ligands such as diethyldithiocarbamate. Moreover, anti-cancer compounds probably interact with proteins, such as HSA, before passing the cancerous cell membrane and DNA as a target. So, the function of proteins and their stabilities are expected to change. In this research, the mode of binding of [Pt (bpy) (amyl.dtc)]NO3 complex with BSA was evaluated by various thermodynamic methods. Negative binding enthalpy and entropy changes amounts show that the connection between the Platinum compound and BSA occurs via the van Der Waals type of hydrogen bond. The negative Gibbs free energy change was obtained through isothermal titration, which showed interaction proceeds spontaneously. Moreover, the emission titration data showed that protein fluorescence quenching by platinum agent titration is static. Binding, quenching constants, and binding site number were obtained by the Stern-Volmer equation, and only one binding site was determined for this interaction. A Scatchard plot with a positive slope shows the Pt agent-BSA formation is proceeding positively cooperative. The kinetic study displayed that the absorption monitoring followed the second-order model. Finally, molecular docking simulation showed that the position of the Pt agent on protein is placed I under region II.


Introduction
Cancer, which occurs with the uncontrolled growth and proliferation of cells in a part of the body, results from environmental * Corresponding author.** Corresponding author.
Contents lists available at ScienceDirect Heliyon journal homepage: www.cell.com/heliyonhttps://doi.org/10.1016/j.heliyon.2023.e20090Received 4 June 2023; Received in revised form 11 September 2023; Accepted 11 September 2023 factors and genetic disorders; today, it is considered the main cause of death in the world [1,2].Cisplatin is one of the inorganic compounds still sold as an anti-cancer drug; However, in general, this class of drugs is associated with side effects such as gastrointestinal complications and has high treatment costs [3].Although cisplatin has a good effect on some cancers (such as ovarian and stomach cancer), it has an irreversible destructive effect.It affects the kidneys, and its side effects include toxic effects on kidneys, hair loss, hemolytic anemia, nerve damage, and electrolyte imbalance, and its use is limited due to these toxic effects.Therefore, its performance can be improved by reducing the side effects and increasing the drug level [4,5].Cisplatin can bond with biomolecules containing S atoms, which inactivates it and reduces toxicity [6][7][8].So, many ligand and metal compounds have been synthesized and reported as anti-oxidants, anti-esterases, and anti-cancer agents [9][10][11][12].Therefore, using various metals in anti-cancer agents, like Pd, can lead to fewer side effects and toxicity than platinum compounds.Also, using compounds with sulfur-donating ligands, such as thiosulfate or diethyldithiocarbamate [6,13,14].One of the most abundant proteins in plasma is albumin, whose role is to regulate blood osmotic pressure, and its interaction with small molecules provides useful information about the properties of the complex.The structure of this protein is spherical, which is responsible for binding and transporting various small ligands in the blood [15].Bovine serum albumin is one of the proteins that has been studied extensively.BSA has been widely used as a typical protein to peruse the aggregation process of proteins [16][17][18].Amyloid nanofibers obtained from bovine serum albumin have been used as one of the most important carriers of medicinal substances in chemotherapy, including cancer, and due to their high binding capacity, they are of great interest for both hydrophilic and hydrophobic drugs.BSA, as a carrier protein, has three homologous (II, I, and III) domains, (L9-L1) Loops, and two related to subdomains A and B [19][20][21].
Molecular docking studies are used in drug design and discovery and are important for understanding biological regulatory mechanisms.Since these interactions take place through a specific site on the surface of the macromolecule, to understand their function, we need information about ligand-or complex-protein formation, which can include information such as the number of sets of binding sites and how many binding sites there are in each set.In this study, [Pt(bpy)(amyl.dtc)]NO 3 (Scheme 1) was selected as an anti-cancer agent, and its interaction with BSA was evaluated by using experimental spectroscopic methods (UV-Vis and fluorescence spectroscopy) based on the report [22], and theoretical docking simulation.The synthesis method and structural data have been presented in Ref. [23].Cooperativity, the number of binding sites, the Stern-Volmer constant, and thermodynamic and kinetic parameters were evaluated by spectral methods.In addition, the molecule was optimized and analyzed to determine the binding ability and the mode of binding on BSA by a simulation study.

Material and methods
Recently, [Pt(bpy)(amyl.dtc)]NO 3 complex has been synthesized and reported as an anti-cancer drug [23].All materials used in this study were purchased from Sigma-Aldrich (USA).Bovine serum albumin manufactured by Sigma A3782-100 MG was used to prepare BSA solution (1 mg/1 mL Tris buffer).The absorption monitoring was done between 200 and 700 nm by a PerkinElmer Accurately Lambda 25 spectrophotometer (USA).Also, all emissions were detected by a Scinco FS-2 fluorescence spectrophotometer (Korea).

Experimental bovine serum albumin binding 2.2.1. Isothermal titration study
To investigate bovine serum albumin-Pt agent formation, UV absorption was measured in the range of 200-400 nm [22,24].The protein absorptions were monitored in the absence and presence of various dosages of the Pt complex at 27 and 37 • C.

Thermal stability study
In this step, Tm, the temperature at which half of BSA unfolded, was evaluated [25,26].The absorption of both Solutions of BSA (2 mg/mL) and BSA-[Pt(bpy)(amyl.dtc)]NO 3 were detected at 278 nm by the temperature increasing from 25 to 60 • C, separately, where the complex concentration is 1 mM.

Fluorescence spectroscopy
To record the fluorescence emission spectrum of BSA, the range of the fluorescence spectrum was adjusted between 200 and 700 Scheme 1. Structure of [Pt(bpy)(amyl.dtc)]NO 3 complex.
nm (λex = 280 nm), and the width of the excitation and emission gap was set to 5 nm [27][28][29].1500 μl of 0.2 mg/mL BSA solution was placed in the cell, and its emission spectrum was followed by titration of 50 μL Pt agent (10 − 6 M) injection, and the emission spectrum was recorded.

BSA-Pt complex computer simulation
One of the promising technologies in the drug development process is computer-aided drug discovery [30][31][32].The advanced AutoDock program is one of the most important molecular docking software at the international level, which is very useful in the discovery and rational development of pharmaceutical molecules.This software can calculate the number and type of chemical interactions between the ligand and the macromolecular receptor (proteins or nucleic acids) based on the binding free energy using force field functions.Before any simulation, the structure of the complex must be optimized.To get the most stable conformations of the Pt complex the structure-optimizing calculations were carried out by applying DFT/B3LYP method with 6-31G and LANL2DZ basis sets [33].Pt (II) complex was used as a ligand, and BSA as a receptor in the molecular docking.BSA protein with PDB ID: 4F5S was downloaded as a PDB file from the protein database.Interaction of the BSA with Pt (II) complex was performed by the molecular docking program AutoDock 4.2.3 package.To perform molecular docking, the first box building was done with the maximum box size to perform blind docking, and by analyzing the results, the box size and the binding site of the complex to the protein were determined.The main docking and the final analysis were then performed.

Binding isotherm of BSA to Pt-complex
Serum albumins are the carriers of numerous drugs.Because of sharp absorption at 280 nm [34], UV/Vis methods make it easy to study to obtain more information on drug-protein interactions.Fig. 1 shows the UV-vis monitoring of BSA in the attendance and absence of various concentrations of the [Pt(bpy)(amyl.dtc)]NO 3 complex.The decreasing trend in the diagram (Fig. 1a and b) shows that a new complex protein is formed.By using the A max diagram in terms of ʋ،(ʋ = [complex] b /[BSA] t ), the values of L 1/2 (the amount of the complex which can make half of BSA abnormal) were obtained.The less dosage leads to fewer side effects if this complex is used as a medicine in cancer treatment [35].Different thermodynamic parameters such as the binding constant, K b , and the standard binding Gibbs free energy changes, ΔG • b , can be obtained according to equations ( 1) and ( 2) [34]: ) . ( In equation ( 1), A 0 is, the initial absorbance of free BSA, A ∞ is the final absorbance of bound BSA at 280 nm, and A is the measured absorbance at particular complex concentrations (Fig. 2a and b).By drawing the plot of 1/A-A 0 vs 1/[complex], Fig. 2a′ and 2b′, the binding constant was obtained.According to these graphs and the binding constant reported in Table 1, it can be concluded rising temperature leads to decreasing binding constant, and the larger binding constant shows a strong interaction between the Pt complex and BSA protein [31].To compare this data with a clinical Pt drug, cisplatin, this investigation was done with Human Serum Albumin, HSA, at room temperature [35], reported in Fig. 3a and b, respectively.According to Figs. 2 and 3, K b can be obtained.With the help of ΔG • b and K b values, other thermodynamic parameters were determined through the van't Hoff condition [36] (equations ( 3) and ( 4)): Thermodynamic parameters are presented in Table 1.According to these values, the type of connection can be determined [36].The results display that the main forces driving the interaction are van der Waals and hydrogen binding forces [37].

Binding isotherm
The binding analysis of experimental data is done by binding isotherms and Scatchard diagrams, which are always associated with problems.Still, one fact that is very popular today is the concept of binding capacity [38].The binding capacity can be gotten using
[Pt (bpy) (amyl.dtc)]NO 3 300 0.  equation ( 5) [38]: Where ʋ is defined by equation ( 6) [22] as follows: Therefore, considering the slope of the isotherm plot (Fig. 4), the binding capacity value can be obtained.Since the binding isotherms drawn at two temperatures are single steps, this system has one binding set [38].Equation ( 5) can be rewritten to the linear form (equation ( 7)) as follow: In this expression, n H is called the Hill coefficient.According to this equation, if a system is identical and dependent, the diagram of RTθ/ʋ vs ʋ should be linear (Fig. 5a and b).
Due to the linearity of the binding capacity diagram, RTθ/ʋ in terms of ʋ, only one proper set of binding sites was observed on BSA for this complex [39].

Binding analysis with scatchard diagram
By drawing the Scatchard plot (υ/[L] vs υ), we can obtain main data on protein binding with drugs, such as the number of binding sites and the binding constant.So, if this graph is linear, it is non-cooperative; if the slope of the graph is positive and the curve of the graph is downward, it shows positive cooperation, and the opposite case shows negative cooperation.The Scatchard diagram is drawn for the interaction of this complex with bovine serum albumin at two temperatures of 27 and 37 • C (Fig. 6).We use Hill's equation (equation ( 8)) to obtain Hill binding constant, K H, and Hill coefficient, n H, as follows [6]: Considering the positive slope of the graph and the low depression of the graphs, it can be concluded that this interaction proceeds via a positive, cooperative mechanism [6,40].
By drawing the graph of Ln (ʋ/g-ʋ) in terms of Ln [complex] f (Fig. 7), Hill's constant, K H , and Hill's coefficient, n H , were obtained.These values are reported in Table 2.In these graphs, the Hill coefficient is more than one at 27 and 37 • C, with positive, cooperative behavior in this interaction [41].
The values related to molar and binding Gibbs free energy are obtained through equation ( 9) as follow [38,42]: Fig. 8 shows the graph of molar binding Gibbs free energy changes versus Ln [complex] f at both mentioned temperatures.The negative slope indicates positive cooperativity in related interactions [43].

BSA thermal stability
The thermal stability of protein can be studied based on [L] 1/2 value and the ratio of [L]/[BSA] [42] in the absence and presence of the drug.T m was determined by UV scanning of 2 mg/mL solution of BSA at 278 nm in the presence and absence of 10 − 4 M Platinum agent.In this test, the temperature increased from the ambient temperature by 1 • C per minute until it reached 60 • C. The value of Tm

Table 2
Hill parameter and binding constant of BSA interaction with complex.for the BSA in the presence of the platinum agent is about 47 • C, while this value is only about 37 • C for the protein (Fig. 9a).This study was repeated using cisplatin as a controller, and HSA thermal changing was continued to 95 • C (Fig. 9b) [35].The results show Pt complex-BSA formation leads to a stable system [42].

UV-visible kinetic study
Kinetic studies consider arranged information about the binding mode of BSA with Pt agent by the time checking recorded 1 min at 278 nm wavelength until 1 h (Fig. 10a and b) [39,43].Based on equations ( 10) and ( 11) and plotting the charts vs time (seconds), the rate constant of the BSA-Pt agent can be determined.
In these two formulas, A 0 is initial absorption, A ∞ is final absorption, A is absorption in successive times, k is a rate constant, and t is time.To determine the order type of the mechanism in the interaction of the above complex with bovine serum albumin, the following graphs were drawn at two temperatures of 27 and 37 • C (Fig. 11a and b).According to equations (10) and (11), since the square linear regression coefficient, R 2 , in these graphs is more linear for the second-order reaction than the first-order reaction, it is concluded that the kinetics is a second-order type for both 27 and 37 • C during occupying of all binding sites.In biological systems, protein interaction should depend on drug and protein concentrations in binding.So, it will lead to limit protein binding and interaction with drugs.It means probably side effects decrease since this matter is important in research in the drug design field [44].

BSA emission quenching
Bovine serum albumin has amino acids that have fluorescent properties, so fluorescence spectroscopy is widely used to evaluate its interaction with metal compounds [43].There are two types of tryptophan in BSA: tryptophan 212, which is in the hydrophobic part, and tryptophan 134, which is on the molecule's surface [44,45].So, fluorescence emission monitoring was done for BSA-free and BSA-complex systems, and decreasing intensity was observed, along with increasing complex concentration, in the BSA-Pt agent.In this test, we set the excitation wavelength to 280 nm (Fig. 12), and the quenching indicates drug binding to the protein [22].
The Stern-Volmer equation (equation ( 12)) was utilized to evaluate the experimentally obtained emission data, and the fluorescence quenching proceed [6,40,41]: In this relationship, F o , F, τ 0 , Q, k q , K sv, and n are fluorescence emissions in the absence and presence of the Pt complex, the lifetime (10 − 8 s) of the fluorophore within the nonappearance of Pt agent, as ligand, which is equal to, the concentration of the ligand, the rate constant; and quenching constant and binding site numbers on protein, respectively [46].To obtain K sv , low concentration regions are considered at the ratio of 1:1 (ligand/protein), and linear F o /F plot vs [Q] in various by reducing the fluorescence emission.Based on Ksv = kq.τequation, kq is also calculated (more than 2 × 10 10 M − 1 S − 1 ), and static interaction is confirmed [47,48].
Using different methods, K b and the number of binding sites per protein molecule can be determined by equation (13), which has been applied as follows:

Molecular docking study
The advanced AutoDock program is one of the most important docking simulation software at the international level, which is very useful in the discovery and rational development of pharmaceutical molecules.Using force field functions, this software can calculate the chemical interactions between the ligand and the macromolecular receptor (proteins or nucleic acids) based on the binding free energy [52,53].The BSA code, which was downloaded, is 4F5S from the PDB.During the data analysis, the appropriate grid size was set with a distance of 0.375 Å along the three axes.Concurring with the Gibbs energy, the restraint consistency was calculated, and the   esteem of K i for the Pt agent was 41.29 nM (nanomolar).As shown in Fig. 14, there was no hydrogen bound.In this interaction, one hydrogen bond with the amino acid glutamine and eight hydrophobic bonds with the amino acids alanine, asparagine, glycine, lysine, phenylalanine, and valine were observed.The comes about of molecular docking indicates the binding position of the Pt compound on BSA site I within the subdomain IIA.

Conclusions
Cisplatin treats human cancers such as bladder and ovarian cancer, head and neck cancer, and testicular cancer.But its clinical utilization is constrained due to a few genuine side impacts.Hence, it is conceivable to utilize S, S giver ligands such as dithiocarbamate to get ready anti-cancer drugs and decrease a few side impacts.In this research, the interaction ability of [Pt (bpy) (amyl.dtc)]NO 3 with BSA was investigated by using fluorescence emission titration, UV-Vis.absorption monitoring, and molecular docking simulation.Thermodynamic parameters were obtained.The enthalpy and entropy values were − 62.1, − 133.58 kJ/mol, and − 126.91 kJ/mol .K at 27 and 37 • C, respectively, which display that the driving forces during the interaction are van der Waals and hydrogen binding.The   negative Gibbs free energy obtained showed a spontaneous interaction.Using the spectroscopic kinetic model, the linear regression coefficient in the graph for the second-order reaction is higher than the first-order reaction, so it can be concluded that the kinetic prefers second order, and binding of the complex on BSA depends on drug and protein concentrations.Moreover, the emission titration results showed that protein fluorescence quenching by the Pt complex is a static quenching mechanism by the Stern-Volmer equation.The results showed that there is only one binding site in the interaction of the complex with BSA.Molecular docking showed that the location of this complex on BSA is position I under region IIA.